Abstract 5319: Treatment of K562 leukemia cells with an experimental UBE2K modifier identifies multi-omic changes associated with altered oncogenic processes
Authors: Punit Shah, Richard Searfoss, Valerie Bussberg, Bennett Greenwood, Shraddha Karmacharya, Allison MacDonald, Kennedy Ofori-Mensa, Vladimir Tolstikov, Pragalath Sundararajan, Maria-Dorothea Nastke, Eric M. Grund, Gregory M. Miller, Stephane Gesta, Rangaprasad Sarangarajan, Elder Granger, Niven R. Narain, Vivek K. Vishnudas, Michael A. Kiebish
Journal: Cancer Research (2022)

Abstract Ubiquitination is a conserved post translation modification involving covalent attachment of ubiquitin protein and is known to regulate many biological processes, including proteasomal degradation. Three major families of enzymes are involved in the regulation of ubiquitination, including activating enzyme E1, Ubiquitin conjugating enzyme E2 and ubiquitin ligase E3. UBE2K is an E2 conjugating ligase that was identified as an anti-cancer drug target from the BERG Interrogative Biology® platform, an artificial intelligence multi-omics analytical method employing Bayesian algorithms. Herein, we used proteomics, lipidomics and metabolomics to investigate the impact of the treatment of UBE2K small molecule ligand (BRG0451) on K562 leukemia cells. K562 cells were treated with 30, 100 and 300 nM concentrations for 24 hours with BRG0451 or Paclitaxel or 0.1% DMSO (Control). Cells were pelleted and analyzed using a multi-omics approach. Proteomic analysis was performed using Thermo Q-Exactive+ LC MS/MS analysis. Lipidomic analysis was performed using SCIEX TripleTOF MS/MS ALL shotgun workflow and metabolomics was performed using 3 different platforms (High resolution RP-LC-MS, HILIC QqQ LC-MS/MS and GC-TOF MS). Unsupervised clustering and differential analysis were used to investigate the impact of the treatments. Proteomic analysis identified and quantified 6930 proteins from K562 cells using TMT labelling with offline 24 fractions and LC-MS/MS. Structural lipidomics analysis evaluated 1980 lipid molecular species and metabolomics analysis identified over 700 metabolites using GC-MS, LC-MS and LC-MS/MS. Multiomics and regression analysis for 30 nM BRG0451 treatment revealed no distinct pattern of omics variables. However, treatment on K562 cells with 300 nM treatment demonstrated 97 differentially expressed proteins compared to control. Pathway analysis revealed chromatin remodeling, and more specifically, regulation of chromatin silencing and localization to nucleolus as major pathways impacted by differentially expressed proteins. Similar pathways were impacted by Paclitaxel and Nocodazole treatment compared to control. Additionally, metabolomic and lipidomic differentials were observed with 300 nM BRG0451 treatment. Structural lipidomics revealed dose -dependent changes in triacylglycerols and cholesterol esters, glycolipid monounsaturated species, and glycolipid medium carbon chain subgroups. Dose dependent impact on amino acids metabolism, purine metabolism, and pyrimidine metabolism was observed with a high degree of similarity for compared drugs. Herein, we demonstrated the use of multi-omics technology in deconvoluting the impact of BRG0451 on independent biological pathways, revealing the intricate mechanisms targeting cell cycle as well as ubiquitin regulator components in a leukemia cell line. Citation Format: Punit Shah, Richard Searfoss, Valerie Bussberg, Bennett Greenwood, Shraddha Karmacharya, Allison MacDonald, Kennedy Ofori-Mensa, Vladimir Tolstikov, Pragalath Sundararajan, Maria-Dorothea Nastke, Eric M. Grund, Gregory M. Miller, Stephane Gesta, Rangaprasad Sarangarajan, Elder Granger, Niven R. Narain, Vivek K. Vishnudas, Michael A. Kiebish. Treatment of K562 leukemia cells with an experimental UBE2K modifier identifies multi-omic changes associated with altered oncogenic processes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5319.